• Journal of Species Research
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• v.7 no.2
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• pp.123-134
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• 2018

A total of 22 bacterial strains belonging to the phylum Bacteroidetes were isolated primarily from aquatic environments such as seawater, freshwater, lagoon and tidal flat. One of these 22 strains was isolated from ginseng soil. Phylogenetic analyses based on 16S rRNA gene sequences revealed that 21 strains showed the high sequence similarities(${\geq}98.7%$) to the closest type strains and formed robust phylogenetic clades with closely related species in the phylum Bacteroidetes. One strain, which had been previously classified as Balneola vulgaris in the phylum Bacteroidetes, was identified as a member of the newly described phylum Rhodothermaeota. These strains had not been previously reported in Korea. Here, we report 21 species of 13 genera in the phylum Bacteroidetes and one species in the phylum Rhodothermaeota which were not reported in Korea. Morphological, biochemical, and physiological characteristics, isolation sources, and NIBR deposit numbers are described in the species descriptions.

• Journal of Microbiology and Biotechnology
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• v.19 no.11
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• pp.1281-1287
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• 2009

The distribution pattern of the phylum Acidobacteria, a previously uncultured bacterial group, was investigated by molecular ecological analyses of global soil samples collected from pristine ecosystems across five continents. Acidobacterial 16S rDNAs were observed in almost all soil samples, and members of acidobacterial primer group A were detected in all samples that harbored the phylum Acidobacteria. Other primer groups, Y, G, and O, showed limited distribution patterns. We further divided the primer groups into acidobacterial subdivisions (class-level). Subdivisional distribution patterns were determined by comparing the observed T-RFs with theoretical T-RFs predicted by in silico digestion of acidobacterial 16S rDNAs. Consistent with the PCR results obtained with subgroup-specific primers, T-RFLP analyses showed that acidobacterial subdivision 1 belonging to primer group A was present in the majority of the soil samples. This study revealed that the phylum Acidobacteria could be globally distributed. At the subdivisional level, acidobacterial subdivision 1 might be the most widely distributed group in this phylum, indicating that members of subdivision 1 might be adapted to various soil environments, and members belonging to other subdivisions might be restricted to certain geographic regions or habitats.

• Journal of Species Research
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• v.12 no.4
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• pp.374-414
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• 2023

As part of a comprehensive investigation of indigenous prokaryotic species in Republic of Korea in 2022, 156 bacterial strains were isolated from diverse environmental habitats. These strains were assigned to six phyla, namely Acidobacteriota, Deinococcota, Actinomycetota, Bacillota, Bacteroidota, and Pseudomonadota. Each strain was identified based on 16S rRNA gene sequence similarity (>98.7%) and the formation of robust phylogenetic clades with their closest reported species. Among isolates, there is one species belonging to the phylum Acidobacteriota, one species belonging to the phylum Deinococcota, 28 species belonging to the phylum Actinomycetota, 19 species belonging to the phylum Bacillota, 19 species belonging to the phylum Bacteroidota, and 88 species belonging to the phylum Pseudomonadota (comprising 34 species of the class Alphaproteobacteria, 20 species of the class Betaproteobacteria, and 34 species of the class Gammaproteobacteria). Based on 16S rRNA gene sequence analysis, each strain was assigned to independent and predefined bacterial species. Since there were no published or official reports regarding these 156 isolates in Republic of Korea, they are reported as unrecorded species in Republic of Korea. The Gram stain, colony and cell morphology, basic biochemical characteristic, isolation source, and strain ID of each species are described in the species descriptions.

• Journal of Species Research
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• v.6 no.1
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• pp.25-41
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• 2017

As a subset study for the collection of Korean indigenous prokaryotic species, 62 bacterial strains belonging to the phylum Actinobacteria were isolated from various sources. Each strain showed higher 16S rRNA gene sequence similarity (>98.75%) and formed a robust phylogenetic clade with closest species of the phylum Actinobacteria which were defined with valid names, already. There is no official description on these 62 actinobacterial species in Korea. Consequently, unrecorded 62 species of 25 genera in the 14 families belonging to the order Actinomycetales of the phylum Actinobacteria were found in Korea. Morphological properties, basic biochemical characteristics, isolation source and strain IDs are described in the species descriptions.

• Journal of Species Research
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• v.10 no.3
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• pp.217-226
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• 2021

During a project aiming to comprehensively investigate indigenous prokaryotic species in Korea, a total of 20 bacterial strains phylogenetically belonging to the the class Bacilli of the phylum Firmicutes were isolated from various environmental sources such as soil, air, tidal flat, sea water, grain, wetland, breast milk and healthy human urine. Phylogenetic analysis based on 16S rRNA gene sequences revealed that 20 bacterial strains showed the high sequence similarities (≥98.7%) to the closest type strains and formed robust phylogenetic clades with closely related species of validly published names in the class Bacilli of the phylum Firmicutes. In the present study, we report 20 species of 13 genera of seven families of two orders of one class in the phylum Firmicutes, which have not been previously reported in Korea. Morphological, biochemical, and physiological characteristics, isolation sources, and NIBR deposit numbers of these unrecorded bacterial species are described in the species descriptions.

• Journal of Species Research
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• v.10 no.4
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• pp.321-335
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• 2021

In 2020, a total of 12 bacterial strains were isolated from soil after a comprehensive investigation of indigenous prokaryotic species in Korea. It was determined that each strain belonged to independent and predefined bacterial species, with high 16S rRNA gene sequence similarity (>98.7%) and formation of a robust phylogenetic clade with the closest species. This study identified four families in the phylum Actinobacteria, two families in the phylum Proteobacteria, one family in the phylum Bacteroidetes one family in the phylum Firmicutes; and four species in the family Nocardiaceae, two species in the family Nocardioidaceae, one species in the family Cellulomonadaceae, one species in the family Hymenobacter, one species in the family Methylobacteriaceae, one species in the family Microbacteriaceae, one species in the family Bacillaceae and one species in the family Sphingomonadaceae. There is no official report of these 12 species in Korea, so they are described as unreported bacterial species in Korea in this study. Gram reaction, basic biochemical characteristics, colony, and cell morphology are included in the species description section.

• Journal of Species Research
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• v.8 no.2
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• pp.197-214
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• 2019

The taxonomic hierarchy of the phylum Proteobacteria was assessed, after which the isolation and classification state of Proteobacteria species with valid names for Korean indigenous isolates were studied. The hierarchical taxonomic system of the phylum Proteobacteria began in 1809 when the genus Polyangium was first reported and has been generally adopted from 2001 based on the road map of Bergey's Manual of Systematic Bacteriology. Until February 2018, the phylum Proteobacteria consisted of eight classes, 44 orders, 120 families, and more than 1,000 genera. Proteobacteria species isolated from various environments in Korea have been reported since 1999, and 644 species have been approved as of February 2018. In this study, all novel Proteobacteria species from Korean environments were affiliated with four classes, 25 orders, 65 families, and 261 genera. A total of 304 species belonged to the class Alphaproteobacteria, 257 species to the class Gammaproteobacteria, 82 species to the class Betaproteobacteria, and one species to the class Epsilonproteobacteria. The predominant orders were Rhodobacterales, Sphingomonadales, Burkholderiales, Lysobacterales and Alteromonadales. The most diverse and greatest number of novel Proteobacteria species were isolated from marine environments. Proteobacteria species were isolated from the whole territory of Korea, with especially large numbers from the regions of Chungnam/Daejeon, Gyeonggi/Seoul/Incheon, and Jeonnam/Gwangju. Most Halomonadaceae species isolated from Korean fermented foods and solar salterns were halophilic or halotolerant. Air-borne members of the genera Microvirga, Methylobacterium, and Massilia had common characteristics in terms of G+C content, major respiratory quinones, and major polar lipids.

• Journal of Species Research
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• v.12 no.4
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• pp.415-429
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• 2023

As part of a comprehensive investigation of indigenous prokaryotic species in the Republic of Korea, 37 bacterial strains belonging to 36 species were isolated from diverse environmental habitats. These strains were assigned to five phyla, namely Deinococcota, Actinomycetota, Bacillota, Bacteroidota, and Pseudomonadota. Each strain was identified based on 16S rRNA gene sequence similarity (>98.7%) and the formation of definite phylogenetic clades with their closest reported species. Among isolates, there is one species belonging to the phylum Deinococcota, five species belonging to the phylum Actinomycetota, four species belonging to the phylum Bacillota, nine species belonging to the phylum Bacteroidota, and 17 species belonging to the phylum Pseudomonadota (comprising eight species of the class Alphaproteobacteria, one species of the class Betaproteobacteria, and eight species of the class Gammaproteobacteria). Based on 16S rRNA gene sequence analysis, each strain was assigned to independent and predefined bacterial species. Since there were no published or official reports regarding these 36 species in the Republic of Korea, they have been reported as unrecorded species in the Republic of Korea. Their Gram stain, cell morphology, colony, basic biochemical characteristics, strain ID, and isolation source of each species are described in the species descriptions.

• Korean Journal of Environmental Biology
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• v.41 no.3
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• pp.215-222
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• 2023

In 2022, research for native prokaryotic species in Korea reported 10 unrecorded bacterial strains affiliated to phyla Actinomycetota, Bacillota, and Pseudomonadota. The strains formed monophyletic clades with the most closely related species (with ≥98.7% sequence similarity) in the 16S rRNA gene sequencing. Among them, four species of the phylum Actinomycetota, two species of the phylum Bacillota, and four species of the phylum Pseudomonadota have not been reported in Korea, suggesting unrecorded species in Korea. Information on strains such as Gram staining reaction, colony and cell morphology, biochemical characteristics, and isolation sources were provided in the species description.

• Journal of Life Science
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• v.28 no.3
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• pp.361-368
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• 2018

This study investigated the diversity of communities of intestinal microorganisms, separated from the intestinal organs of Red tilefish (Branchiostegus japonicas), collected on the Jeju Coast. First, in the isolation of 1.5% BHIA, MA, TSA and R2A Agar on the medium, there were most colonies in 1.5% BHIA. The results of aerobic culture and anaerobic culture were $1.7{\times}10^6CFU/g^{-1}$ and $1.1{\times}10^5cfu/g^{-1}$, respectively, on average, and 147 pure colonies were separated in total. In 16S rDNA sequencing, there were 58 genera and 74 species, showing 95-100% similarity with the basic strain. They were divided broadly into 5 phyla, and as the main phyletic group, Proteobacteria phylum comprised 50% with 9 families, 35 genera and 35 species of Moraxellaceae, Rhodobacteraceae, Shewanellae, Halomondaceae, Enterobacteriaceae, Vibrionaceae, Hahellaceae, Pseudomonadaceae, and Erythrobacteraceae, with the highest index of dominance. Actinobacteria phylum comprised 24% with 8 families, 11 genera and 17 species of Microbacteriaceae, Intrasporangiaceae, Dietziaceae, Dermabacteraceae, Dermacoccaceae, Nocardiodaceae, Brevibacteriaceae and Propionobacteriacea; Firmicutes phylum, 16% with 6 families, 8 genera and 17 species of Bacillaceae, Staphylcoccaceae, Planococcaceae, Streptococcaceae, Paenibacillaceae and Clostridiaceae; Bacteroidetes phylum, 6% with 2 families, 3 genera and 4 species of Cyclobacteriaceae and Flavobacteriaceae; and Deinococcus-Thermus phylum, 4% with 1 family, 1 genus and 1 species of Deinococcaceae.